Contacts of the helix formed by residues 1019 - 1024 (chain C) in PDB entry 6DBT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS1019 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588C ASP* 3.9 5.7 + - - +
589C LEU* 3.6 31.9 - - + -
591C GLU* 5.5 2.5 - - - +
592C ASP* 4.0 22.2 - - - +
663C PHE* 5.5 7.2 - - - -
665C GLU* 3.7 20.5 + - - -
672C LEU 5.0 3.4 + - - -
673C SER* 4.6 10.2 + - - -
675C ARG* 4.8 3.0 - - - +
1018C SER* 1.3 78.2 + - - +
1020C TYR* 1.3 66.1 + - - +
1022C GLN* 3.0 28.8 + - + +
1023C LYS* 3.1 33.5 + - + +
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Residues in contact with TYR1020 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C HIS* 4.1 11.8 + - - -
484C ALA* 4.2 9.1 - - + +
529C LEU* 4.0 31.2 - - + -
588C ASP* 3.2 23.4 + - - +
1018C SER* 3.2 4.9 + - - +
1019C LYS* 1.3 78.3 - - - +
1021C LEU* 1.3 63.7 + - + +
1022C GLN 3.1 1.4 + - - -
1023C LYS* 3.2 18.5 + - + +
1024C PHE* 3.2 47.5 + + - +
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Residues in contact with LEU1021 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C ALA* 4.6 9.6 - - + +
487C LEU* 3.7 33.0 - - + -
488C ALA* 3.9 27.2 - - + +
491C VAL* 6.4 1.1 - - + -
529C LEU* 3.6 29.6 - - + -
1015C LEU* 4.0 25.6 - - + +
1018C SER* 3.2 30.1 - - - +
1019C LYS 3.4 0.8 - - - -
1020C TYR* 1.3 79.2 - - + +
1022C GLN* 1.3 60.6 + - + +
1024C PHE* 3.9 9.9 + - - +
1025C MET* 3.5 17.3 + - - +
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Residues in contact with GLN1022 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492C ASN* 6.3 0.7 - - - +
672C LEU* 3.2 54.7 + - - +
1016C TYR* 3.6 21.0 - - + +
1018C SER 3.1 22.0 + - - +
1019C LYS* 3.0 26.8 + - + +
1021C LEU* 1.3 79.2 - - + +
1023C LYS* 1.3 65.7 + - + +
1024C PHE 3.3 0.2 - - - -
1025C MET* 2.7 35.0 + - + +
1026C GLU* 4.6 0.2 - - - -
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Residues in contact with LYS1023 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591C GLU* 5.1 18.3 + - - +
592C ASP* 5.2 9.3 + - - -
1019C LYS* 3.1 35.3 + - + +
1020C TYR* 3.2 11.9 + - + +
1022C GLN* 1.3 80.2 - - + +
1024C PHE* 1.3 61.9 + - + +
1025C MET 3.1 1.0 + - - -
1026C GLU* 3.2 40.3 + - - +
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Residues in contact with PHE1024 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A THR* 4.8 1.6 - - - +
510A THR* 4.2 9.2 + - + -
482C HIS* 3.7 28.3 - + + -
484C ALA* 3.4 28.9 - - + -
485C VAL* 3.3 39.8 - - + +
488C ALA* 5.2 0.7 - - + -
1020C TYR* 3.2 47.7 + + - +
1021C LEU* 4.0 13.0 - - - +
1022C GLN 3.3 0.2 - - - -
1023C LYS* 1.3 78.7 - - + +
1025C MET* 1.3 56.1 + - - +
1026C GLU* 3.4 7.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il